3AX8

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 15alpha-methoxy-1alpha,25-dihydroxyvitamin D3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DB1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.489α = 90
b = 51.585β = 90
c = 132.017γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCD2008-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.000Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.65099.33.5990633
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.794.73.272.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DB12.648.06931947299.320.218440.21490.29369RANDOM15.758
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.05-0.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.782
r_dihedral_angle_4_deg20.832
r_dihedral_angle_3_deg18.314
r_dihedral_angle_1_deg6.277
r_scangle_it3.375
r_scbond_it2.08
r_angle_refined_deg1.814
r_mcangle_it1.469
r_mcbond_it0.888
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.782
r_dihedral_angle_4_deg20.832
r_dihedral_angle_3_deg18.314
r_dihedral_angle_1_deg6.277
r_scangle_it3.375
r_scbond_it2.08
r_angle_refined_deg1.814
r_mcangle_it1.469
r_mcbond_it0.888
r_nbtor_refined0.311
r_nbd_refined0.234
r_chiral_restr0.212
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.131
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2018
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling